chr16-67662462-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001037281.2(PARD6A):c.853G>A(p.Val285Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0373 in 1,613,598 control chromosomes in the GnomAD database, including 1,337 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001037281.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARD6A | NM_001037281.2 | c.853G>A | p.Val285Ile | missense_variant | 3/3 | ENST00000458121.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARD6A | ENST00000458121.7 | c.853G>A | p.Val285Ile | missense_variant | 3/3 | 1 | NM_001037281.2 | A1 | |
PARD6A | ENST00000219255.3 | c.856G>A | p.Val286Ile | missense_variant | 3/3 | 1 | P4 | ||
PARD6A | ENST00000602551.5 | c.766G>A | p.Val256Ile | missense_variant | 3/3 | 5 | |||
PARD6A | ENST00000602727.1 | n.1013G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0297 AC: 4517AN: 152226Hom.: 95 Cov.: 33
GnomAD3 exomes AF: 0.0313 AC: 7832AN: 250442Hom.: 178 AF XY: 0.0319 AC XY: 4320AN XY: 135578
GnomAD4 exome AF: 0.0381 AC: 55710AN: 1461254Hom.: 1242 Cov.: 32 AF XY: 0.0376 AC XY: 27308AN XY: 726928
GnomAD4 genome AF: 0.0297 AC: 4522AN: 152344Hom.: 95 Cov.: 33 AF XY: 0.0282 AC XY: 2098AN XY: 74494
ClinVar
Submissions by phenotype
PARD6A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at